PDB Chemical Component IM5
The following tables include covalent bond distance, bond angle and torsion angle values for the experimental model and ideal geometries stored in the definition for this chemical component.
Bond Distances for IM5
| Atom I |
Atom J |
Distance (Experimental Model) |
Distance (Ideal Model) |
| C2 |
N1 |
1.357 |
1.364 |
| N1 |
C6 |
1.343 |
1.351 |
| N1 |
HN1 |
1.000 |
0.970 |
| N2 |
C2 |
1.343 |
1.374 |
| N3 |
C2 |
1.336 |
1.312 |
| N2 |
HN2 |
1.000 |
0.970 |
| N2 |
HN2A |
1.000 |
0.970 |
| N3 |
C4 |
1.350 |
1.347 |
| C9 |
C4 |
1.467 |
1.412 |
| C4 |
C5 |
1.461 |
1.399 |
| C5 |
N7 |
1.333 |
1.379 |
| C5 |
C6 |
1.478 |
1.408 |
| C6 |
O6 |
1.256 |
1.220 |
| C8 |
N7 |
1.362 |
1.362 |
| C9 |
C8 |
1.387 |
1.348 |
| C8 |
H8 |
1.080 |
1.080 |
| C10 |
C9 |
1.513 |
1.508 |
| C10 |
N1' |
1.442 |
1.469 |
| N1' |
C2' |
1.466 |
1.486 |
| N1' |
C6' |
1.467 |
1.486 |
| C10 |
H10 |
1.100 |
1.090 |
| C10 |
H10A |
1.100 |
1.090 |
| C2' |
C3' |
1.520 |
1.544 |
| C2' |
H2' |
1.100 |
1.090 |
| C2' |
H2'A |
1.100 |
1.089 |
| O3' |
C3' |
1.431 |
1.430 |
| C3' |
C4' |
1.516 |
1.542 |
| C3' |
H3' |
1.100 |
1.090 |
| O3' |
HO3' |
0.950 |
0.967 |
| C6' |
C4' |
1.525 |
1.544 |
| C4' |
C5' |
1.514 |
1.531 |
| C4' |
H4' |
1.101 |
1.091 |
| C5' |
O5' |
1.430 |
1.429 |
| C5' |
H5' |
1.100 |
1.090 |
| C5' |
H5'A |
1.100 |
1.089 |
| O5' |
HO5' |
0.950 |
0.968 |
| C6' |
H6' |
1.100 |
1.090 |
| C6' |
H6'A |
1.100 |
1.090 |
| N7 |
HN7 |
1.000 |
0.969 |
Bond Angles for IM5
| Atom I |
Atom J |
Atom K |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C2 |
N1 |
C6 |
124.0 |
120.4 |
| C2 |
N1 |
HN1 |
118.0 |
119.8 |
| C6 |
N1 |
HN1 |
118.0 |
119.8 |
| N1 |
C6 |
C5 |
117.0 |
118.5 |
| N1 |
C6 |
O6 |
121.4 |
120.8 |
| HN2 |
N2 |
HN2A |
120.0 |
119.9 |
| N3 |
C4 |
C5 |
123.3 |
119.6 |
| C4 |
C5 |
N7 |
106.9 |
107.3 |
| C4 |
C5 |
C6 |
114.9 |
118.7 |
| C6 |
C5 |
N7 |
138.2 |
134.0 |
| C5 |
N7 |
HN7 |
124.4 |
125.7 |
| C5 |
C6 |
O6 |
121.7 |
120.7 |
| C8 |
N7 |
HN7 |
124.4 |
125.6 |
| C9 |
C8 |
H8 |
124.4 |
125.3 |
| C10 |
N1' |
C2' |
111.7 |
111.0 |
| C10 |
N1' |
C6' |
113.4 |
110.9 |
| C2' |
N1' |
C6' |
107.4 |
104.2 |
| N1' |
C2' |
C3' |
100.2 |
104.6 |
| N1' |
C2' |
H2' |
111.7 |
110.3 |
| N1' |
C2' |
H2'A |
111.7 |
110.4 |
| N1' |
C6' |
C4' |
103.1 |
104.6 |
| N1' |
C6' |
H6' |
111.0 |
110.5 |
| N1' |
C6' |
H6'A |
111.1 |
110.4 |
| H10 |
C10 |
H10A |
109.5 |
109.5 |
| C3' |
C2' |
H2' |
111.8 |
110.4 |
| C3' |
C2' |
H2'A |
111.7 |
110.4 |
| C2' |
C3' |
C4' |
105.6 |
105.1 |
| C2' |
C3' |
H3' |
110.8 |
110.3 |
| H2' |
C2' |
H2'A |
109.5 |
110.5 |
| O3' |
C3' |
C4' |
108.8 |
110.3 |
| O3' |
C3' |
H3' |
112.1 |
110.3 |
| C4' |
C3' |
H3' |
110.8 |
110.3 |
| C3' |
C4' |
C5' |
111.2 |
110.3 |
| C3' |
C4' |
H4' |
110.5 |
110.3 |
| C6' |
C4' |
H4' |
110.4 |
110.4 |
| C5' |
C4' |
H4' |
110.5 |
110.2 |
| C4' |
C5' |
O5' |
107.7 |
109.4 |
| C4' |
C5' |
H5' |
109.9 |
109.4 |
| C4' |
C5' |
H5'A |
109.9 |
109.4 |
| O5' |
C5' |
H5' |
109.9 |
109.5 |
| O5' |
C5' |
H5'A |
109.9 |
109.5 |
| C5' |
O5' |
HO5' |
109.5 |
113.9 |
| H5' |
C5' |
H5'A |
109.5 |
109.5 |
| H6' |
C6' |
H6'A |
109.5 |
110.5 |
Torsion Angles for IM5
| Atom I |
Atom J |
Atom K |
Atom L |
Angle (Experimental Model) |
Angle (Ideal Model) |
| C6 |
N1 |
C2 |
HN1 |
180.0 |
180.3 |
| C2 |
N1 |
C6 |
C5 |
359.1 |
0.1 |
| C2 |
N1 |
C6 |
O6 |
180.5 |
179.7 |
| C2 |
N1 |
C6 |
HN1 |
180.0 |
179.7 |
| C4 |
C5 |
C6 |
N1 |
0.5 |
360.0 |
| N1 |
C6 |
C5 |
N7 |
181.2 |
180.0 |
| C5 |
C6 |
N1 |
O6 |
178.6 |
180.4 |
| C2 |
N1 |
HN1 |
C6 |
180.0 |
180.3 |
| HN1 |
N1 |
C6 |
C5 |
179.1 |
180.3 |
| HN1 |
N1 |
C6 |
O6 |
0.5 |
359.9 |
| N2 |
C2 |
N1 |
C6 |
180.5 |
180.1 |
| N2 |
C2 |
N1 |
HN1 |
0.4 |
359.8 |
| N3 |
C2 |
N1 |
C6 |
0.2 |
359.9 |
| N3 |
C2 |
N1 |
HN1 |
180.2 |
179.7 |
| N3 |
C4 |
C5 |
N7 |
180.1 |
180.0 |
| N3 |
C4 |
C5 |
C6 |
0.6 |
360.0 |
| N1 |
C6 |
C5 |
C4 |
0.5 |
360.0 |
| C6 |
C5 |
C4 |
N7 |
180.5 |
180.0 |
| C4 |
C5 |
N7 |
HN7 |
180.3 |
179.9 |
| C4 |
C5 |
C6 |
O6 |
179.1 |
180.4 |
| C4 |
C5 |
N7 |
C6 |
180.7 |
180.0 |
| N7 |
C5 |
C6 |
O6 |
359.8 |
0.4 |
| C8 |
N7 |
C5 |
HN7 |
180.0 |
180.1 |
| C5 |
C6 |
N1 |
HN1 |
179.1 |
180.3 |
| N1 |
C6 |
C5 |
O6 |
181.4 |
179.6 |
| C4 |
C5 |
C6 |
N7 |
179.3 |
180.0 |
| C6 |
C5 |
N7 |
HN7 |
359.6 |
359.9 |
| O6 |
C6 |
N1 |
HN1 |
0.5 |
359.9 |
| N1 |
C6 |
O6 |
C5 |
178.5 |
180.4 |
| O6 |
C6 |
C5 |
N7 |
359.8 |
0.4 |
| C5 |
N7 |
C8 |
HN7 |
180.0 |
179.9 |
| C9 |
C8 |
N7 |
HN7 |
180.5 |
180.0 |
| H8 |
C8 |
N7 |
HN7 |
0.5 |
0.1 |
| C10 |
C9 |
C8 |
H8 |
2.4 |
360.0 |
| C2' |
N1' |
C10 |
C6' |
238.4 |
244.7 |
| C10 |
N1' |
C2' |
C3' |
168.4 |
159.0 |
| C10 |
N1' |
C2' |
H2' |
286.9 |
277.7 |
| C10 |
N1' |
C2' |
H2'A |
49.9 |
40.2 |
| C10 |
N1' |
C6' |
C4' |
200.6 |
201.0 |
| C10 |
N1' |
C6' |
H6' |
319.6 |
319.7 |
| C10 |
N1' |
C6' |
H6'A |
81.7 |
82.2 |
| C10 |
N1' |
C2' |
C6' |
125.0 |
119.5 |
| C2' |
N1' |
C6' |
C4' |
324.6 |
320.5 |
| C2' |
N1' |
C6' |
H6' |
83.6 |
79.2 |
| C2' |
N1' |
C6' |
H6'A |
205.6 |
201.7 |
| C3' |
C2' |
N1' |
H2' |
241.5 |
241.3 |
| C3' |
C2' |
N1' |
H2'A |
118.5 |
118.8 |
| N1' |
C2' |
C3' |
C4' |
326.3 |
336.1 |
| N1' |
C2' |
C3' |
H3' |
206.3 |
217.2 |
| H2' |
C2' |
N1' |
H2'A |
237.0 |
237.5 |
| C10 |
N1' |
C6' |
C2' |
236.1 |
240.5 |
| C6' |
N1' |
C2' |
C3' |
43.4 |
39.5 |
| C6' |
N1' |
C2' |
H2' |
161.9 |
158.3 |
| C6' |
N1' |
C2' |
H2'A |
284.9 |
280.7 |
| N1' |
C6' |
C4' |
H4' |
252.7 |
264.9 |
| H6' |
C6' |
N1' |
H6'A |
237.9 |
237.5 |
| H10 |
C10 |
N1' |
C2' |
161.7 |
310.0 |
| H10 |
C10 |
N1' |
C6' |
283.3 |
65.3 |
| H10A |
C10 |
N1' |
C2' |
43.4 |
189.9 |
| H10A |
C10 |
N1' |
C6' |
165.0 |
305.3 |
| C3' |
C2' |
N1' |
C6' |
43.4 |
39.5 |
| N1' |
C2' |
C3' |
H2' |
118.5 |
118.7 |
| N1' |
C2' |
C3' |
H2'A |
241.5 |
241.2 |
| H2' |
C2' |
C3' |
H2'A |
123.1 |
122.5 |
| O3' |
C3' |
C2' |
C4' |
116.5 |
118.9 |
| O3' |
C3' |
C2' |
H3' |
236.5 |
237.8 |
| C4' |
C3' |
C2' |
H3' |
120.0 |
118.9 |
| C2' |
C3' |
C4' |
C5' |
256.1 |
241.1 |
| C2' |
C3' |
C4' |
H4' |
133.0 |
119.0 |
| H2' |
C2' |
N1' |
C6' |
161.9 |
158.3 |
| N1' |
C2' |
H2' |
C3' |
248.6 |
244.9 |
| N1' |
C2' |
H2' |
H2'A |
124.3 |
122.4 |
| C3' |
C2' |
H2' |
H2'A |
235.7 |
237.5 |
| H2' |
C2' |
C3' |
C4' |
207.8 |
217.4 |
| H2' |
C2' |
C3' |
H3' |
87.8 |
98.5 |
| H2'A |
C2' |
N1' |
C6' |
284.9 |
280.7 |
| N1' |
C2' |
H2'A |
C3' |
111.4 |
115.2 |
| N1' |
C2' |
H2'A |
H2' |
235.7 |
237.6 |
| C3' |
C2' |
H2'A |
H2' |
124.3 |
122.4 |
| H2'A |
C2' |
C3' |
C4' |
84.8 |
94.9 |
| H2'A |
C2' |
C3' |
H3' |
324.8 |
336.0 |
| O3' |
C3' |
C2' |
H2' |
324.3 |
336.3 |
| O3' |
C3' |
C2' |
H2'A |
201.3 |
213.8 |
| C2' |
C3' |
O3' |
C4' |
245.6 |
244.3 |
| C2' |
C3' |
O3' |
H3' |
122.7 |
122.1 |
| C4' |
C3' |
O3' |
H3' |
237.1 |
237.8 |
| O3' |
C3' |
C4' |
C5' |
139.8 |
122.2 |
| O3' |
C3' |
C4' |
H4' |
16.7 |
0.1 |
| N1' |
C6' |
C4' |
C3' |
12.3 |
23.9 |
| C4' |
C3' |
C2' |
H2' |
207.8 |
217.4 |
| C4' |
C3' |
C2' |
H2'A |
84.8 |
94.9 |
| C2' |
C3' |
C4' |
H3' |
240.0 |
241.1 |
| O3' |
C3' |
C4' |
H3' |
123.7 |
122.2 |
| C6' |
C4' |
C3' |
H4' |
240.5 |
241.0 |
| C5' |
C4' |
C3' |
H4' |
123.2 |
122.1 |
| C3' |
C4' |
C5' |
O5' |
168.5 |
185.0 |
| C3' |
C4' |
C5' |
H5' |
288.2 |
305.0 |
| C3' |
C4' |
C5' |
H5'A |
48.7 |
65.0 |
| H3' |
C3' |
C2' |
H2' |
87.8 |
98.5 |
| H3' |
C3' |
C2' |
H2'A |
324.8 |
336.0 |
| C2' |
C3' |
H3' |
C4' |
116.8 |
115.6 |
| O3' |
C3' |
H3' |
C4' |
238.2 |
237.8 |
| H3' |
C3' |
C4' |
C5' |
16.1 |
360.0 |
| H3' |
C3' |
C4' |
H4' |
253.0 |
237.9 |
| HO3' |
O3' |
C3' |
C4' |
294.4 |
177.1 |
| HO3' |
O3' |
C3' |
H3' |
57.3 |
299.3 |
| N1' |
C6' |
C4' |
H6' |
119.0 |
118.8 |
| N1' |
C6' |
C4' |
H6'A |
241.0 |
241.2 |
| C6' |
C4' |
C3' |
H3' |
133.4 |
118.9 |
| C3' |
C4' |
C6' |
H4' |
119.6 |
119.0 |
| C5' |
C4' |
C6' |
H4' |
238.9 |
237.9 |
| C6' |
C4' |
C5' |
H5' |
172.3 |
189.3 |
| C6' |
C4' |
C5' |
H5'A |
292.9 |
309.3 |
| N1' |
C6' |
C4' |
C5' |
131.6 |
142.8 |
| C5' |
C4' |
C3' |
H3' |
16.1 |
360.0 |
| C3' |
C4' |
C5' |
H4' |
236.9 |
237.9 |
| C6' |
C4' |
C5' |
H4' |
121.0 |
122.2 |
| O5' |
C5' |
C4' |
H5' |
240.3 |
240.0 |
| O5' |
C5' |
C4' |
H5'A |
119.7 |
120.0 |
| C4' |
C5' |
O5' |
HO5' |
180.0 |
180.0 |
| H5' |
C5' |
C4' |
H5'A |
239.5 |
240.0 |
| H4' |
C4' |
C3' |
H3' |
253.0 |
237.9 |
| C3' |
C4' |
H4' |
C5' |
123.5 |
122.1 |
| H4' |
C4' |
C5' |
O5' |
291.6 |
307.2 |
| H4' |
C4' |
C5' |
H5' |
51.3 |
67.1 |
| H4' |
C4' |
C5' |
H5'A |
171.9 |
187.1 |
| O5' |
C5' |
C4' |
H4' |
291.6 |
307.2 |
| C4' |
C5' |
O5' |
H5' |
119.7 |
119.9 |
| C4' |
C5' |
O5' |
H5'A |
240.3 |
240.0 |
| H5' |
C5' |
O5' |
H5'A |
120.6 |
120.1 |
| H5' |
C5' |
C4' |
H4' |
51.3 |
67.1 |
| C4' |
C5' |
H5' |
O5' |
241.6 |
240.0 |
| C4' |
C5' |
H5' |
H5'A |
120.8 |
120.0 |
| O5' |
C5' |
H5' |
H5'A |
239.2 |
239.9 |
| H5' |
C5' |
O5' |
HO5' |
60.3 |
60.1 |
| H5'A |
C5' |
C4' |
H4' |
171.9 |
187.1 |
| C4' |
C5' |
H5'A |
O5' |
118.4 |
120.0 |
| C4' |
C5' |
H5'A |
H5' |
239.2 |
240.0 |
| O5' |
C5' |
H5'A |
H5' |
120.8 |
120.1 |
| H5'A |
C5' |
O5' |
HO5' |
299.7 |
300.0 |
| HO5' |
O5' |
C5' |
H5' |
60.3 |
60.1 |
| HO5' |
O5' |
C5' |
H5'A |
299.7 |
300.0 |
| N1' |
C6' |
H6' |
C4' |
245.9 |
244.8 |
| N1' |
C6' |
H6' |
H6'A |
123.0 |
122.4 |
| H6' |
C6' |
C4' |
H4' |
133.7 |
146.1 |
| N1' |
C6' |
H6'A |
C4' |
114.0 |
115.2 |
| N1' |
C6' |
H6'A |
H6' |
237.0 |
237.5 |
| H6'A |
C6' |
C4' |
H4' |
11.7 |
23.7 |